Cloud BioLinux standalone VM with Galaxy included !

[agbiotec]

Hi all,

   I've prepared a Cloud BioLinux standalone VM that boots the Galaxy interface as well, so that

you can acess all the tools with minimal need for command line work. I have two versions, one that

is an OVA (Open Virtual Appliance), that can be imported into VirtualBox (www.virtualbox.org) and

booted on a desktop computer, very simply with a few clicks as described here:

http://www.oracle.com/technetwork/server-storage/vm/template-1482544.html

  Also a .vdi (virtual disk image), that provides more flexibility for advanced users (for VMware, or

Eucalyptus / OpenStack private clouds with qemu conversion - email me for details), but which

can also be imported into VirtualBox:

https://blogs.oracle.com/oswald/entry/importing_a_vdi_in_virtualbox

In either case make sure to set network "Adapter 2" to "Bridged" in VirtualBox as shown on attached

screenshot-1.pdf, so that you can access Galaxy via your own computer's browser (the

Galaxy server runs virtualized inside the VM). Then boot the VM and just select the Ubuntu

user as shown on screenshot-2.pdf (no password required). The Galaxy URL for the fully-featured

server running inside the VM is displayed in pop-up window upon login as shown on screenshot-3.pdf, and

if you paste it in your browser (screenshot-4.pdf), you have a fully Galaxy / Cloud BioLinux server

on your desktop !

  For convenience and because the OVA and .vdi files are big (>7GB), I've splited them and created 

two Unix shell scripts that will download the VMs parts automatically (also attached). If you do not have 

access to a Unix system, you can still download the parts one-by-one manually by entering the s3:// URLs

found inside the scripts in your browser's address bar , though I am not sure how you'd merge the different 

parts on a Windows system for example... nonetheless, email me if that's your case and you could send

me a USB stick that I can copy the VM on and mail it back to you.

Hopefully you'll find this useful please don't hesitate to get back to me with any suggestions !

cheers,

 Ntino

PS if you boot the VM while your computer is on a VPN connection, you might have

trouble accessing the Galaxy server running inside the VM via your desktop browser.

[Brad Chapman]

Ntino;
Awesome, thanks for making these. Would you be up for putting together a
single page with all the downloadable resources you've created we could
link to from the main site? A markdown summary of these in the `doc`
directory would work as a starting place so folks can find them without
reading through the mailing lists.

Brad

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> #!/bin/bash
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.aa
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ab
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ac
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ad
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ae
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.af
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ag
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ah
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ai
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.aj
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ak
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.al
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.am
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.an
> wget s3://cloudbiolinuxvms/cloudbiolinux-galaxy-11-15-2012-ova/Cloud BioLinux 11-25-2012 Release.ova.part.ao
> cat Cloud BioLinux 11-25-2012 Release.ova.part.* >> Cloud BioLinux 11-25-2012 Release.ova
> #!/bin/bash
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.aa
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ab
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ac
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ad
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ae
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.af
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ag
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ah
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ai
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.aj
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ak
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.al
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.am
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.an
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ao
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ap
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.aq
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ar
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.as
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.at
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.au
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.av
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.aw
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ax
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ay
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.az
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.ba
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.bb
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.bc
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.bd
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.be
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.bf
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.bg
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.bh
> wget s3://cloudbiolinux-galaxy-11-25-2012-vdi/Cloud BioLinux 11-25-2012 Release.vdi.part.bi
> cat Cloud BioLinux 11-25-2012 Release.vdi.part.* >> Cloud BioLinux 11-25-2012 Release.vdi

[husker...@gmail.com]

Hello Ntino,

I was attempting to run the shell scripts you posted to download the .ova files but they didn't work. I think the problem lies with the spaces between s3:// url's. But when I tried to correct this by putting in some backslashes I still was not able to download the files. Could you give a some pointer on downloading from a s3 bucket for I can get this Biolinux install,

Thank you,

Jeff  

[agbiotec]

Hello Jeff,

 good catch !  I've updated the scripts for downloading either the ova or vdi, find them attached to this email.

Thanks again and let me know if you find any other bugs.

best,

 Ntino

[Tim]

Hi All,

As there are now several split-up image files on S3, I've had a crack at a general purpose downloader script.  This will grab and assemble either a specific file or a whole directory from S3.  I've tried to make it robust but with BASH scripting that's never easy.

The script does need xmlstarlet installed.  I could make it work with just grep/cut but then I reckon everyone should really have xmlstarlet anyway as it's super-handy.

Ntino - could you give it a test run?  I've tried it myself of course but I never trust my code until others have made it work.

Cheers,

TIM

[Hasan Mirza]

Hi there

Many thanks for the files. I wanted to ask how many parts are there because my download got interrupted several times and I'm not sure if the compiled VOD is correct..?

Cheers

H

[Adam Bazinet]

Hi Ntino,

Thanks for making this available. Can you tell me the easiest way to disable booting the Galaxy interface in this VM? I don't mind if all the Galaxy apparatus is there, I just don't want it to start on boot.

thanks,

Adam